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Magnesium in PDB 5qk0: Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110

Enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110

All present enzymatic activity of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110:
2.7.7.96; 3.6.1.13; 3.6.1.58;

Protein crystallography data

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110, PDB code: 5qk0 was solved by Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å) 77.83 / 1.44
Space group P 1
Cell size a, b, c (Å), α, β, γ (°) 49.672, 60.151, 79.779, 79.37, 80.65, 75.23
R / Rfree (%) 30.6 / 33.8

Other elements in 5qk0:

The structure of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 also contains other interesting chemical elements:

Chlorine (Cl) 1 atom

Magnesium Binding Sites:

The binding sites of Magnesium atom in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 (pdb code 5qk0). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 8 binding sites of Magnesium where determined in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110, PDB code: 5qk0:
Jump to Magnesium binding site number: 1; 2; 3; 4; 5; 6; 7; 8;

Magnesium binding site 1 out of 8 in 5qk0

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Magnesium binding site 1 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg301

b:29.5
occ:1.00
 O A:HOH446 1.9 23.9 1.0
O A:HOH417 2.0 24.1 1.0
O A:HOH401 2.1 27.5 1.0
O A:ALA96 2.1 25.5 1.0
O A:HOH441 2.2 26.0 1.0
OE2 A:GLU116 2.2 30.7 1.0
MG A:MG302 3.2 74.3 1.0
C A:ALA96 3.2 26.3 1.0
CD A:GLU116 3.3 30.7 1.0
OE1 A:GLU116 3.6 31.0 1.0
O A:HOH436 3.9 38.0 0.8
NH2 A:ARG84 4.0 31.6 1.0
NE2 A:GLN82 4.1 35.5 1.0
N A:GLY97 4.1 27.1 1.0
CA A:GLY97 4.1 27.9 1.0
N A:ALA96 4.2 25.8 1.0
CA A:ALA96 4.2 26.1 1.0
OE2 A:GLU112 4.2 29.3 1.0
O A:HOH429 4.2 30.2 1.0
OE1 A:GLN82 4.3 35.3 1.0
O A:HOH462 4.4 35.4 1.0
OE2 A:GLU166 4.4 56.6 1.0
O A:HOH464 4.5 50.1 1.0
CG A:GLU116 4.5 30.6 1.0
CD A:GLN82 4.6 35.0 1.0
CB A:ALA96 4.7 26.0 1.0
CZ A:ARG84 4.9 31.8 1.0
NH1 A:ARG84 5.0 32.0 1.0

Magnesium binding site 2 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 2 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
A:Mg302

b:74.3
occ:1.00
 O A:HOH441 1.9 26.0 1.0
O A:HOH410 2.1 38.4 1.0
OE2 A:GLU166 2.2 56.6 1.0
OE2 A:GLU112 2.3 29.3 1.0
OE2 A:GLU116 2.4 30.7 1.0
O A:HOH438 2.6 47.3 1.0
MG A:MG301 3.2 29.5 1.0
CD A:GLU112 3.3 29.3 1.0
CD A:GLU166 3.3 55.9 1.0
CD A:GLU116 3.4 30.7 1.0
CG A:GLU116 3.6 30.6 1.0
OE1 A:GLU112 3.6 29.2 1.0
O A:HOH401 3.7 27.5 1.0
O A:ALA96 3.7 25.5 1.0
OE1 A:GLU166 3.7 56.9 1.0
OE1 A:GLU116 4.5 31.0 1.0
OE2 A:GLU115 4.5 32.4 1.0
CG A:GLU166 4.6 54.9 1.0
CG A:GLU112 4.6 28.9 1.0
C A:ALA96 4.7 26.3 1.0
O A:HOH446 4.7 23.9 1.0
O A:HOH417 4.8 24.1 1.0
CA A:GLY97 4.8 27.9 1.0
O A:HOH457 4.8 31.8 1.0
O A:HOH464 4.9 50.1 1.0
CB A:GLU112 4.9 28.4 1.0

Magnesium binding site 3 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 3 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg303

b:36.2
occ:1.00
 O B:HOH406 1.9 33.5 1.0
O B:HOH405 2.0 32.3 1.0
O B:HOH443 2.0 33.4 1.0
O B:ALA96 2.2 33.4 1.0
OE2 B:GLU116 2.2 35.4 1.0
O B:HOH434 2.3 37.5 1.0
CD B:GLU116 3.3 36.0 1.0
C B:ALA96 3.4 32.8 1.0
OE1 B:GLU116 3.7 35.3 1.0
OE1 B:GLN82 3.8 37.4 1.0
NH2 B:ARG84 3.9 35.2 1.0
NE2 B:GLN82 4.2 36.6 1.0
N B:GLY97 4.2 33.8 1.0
O B:HOH449 4.2 36.3 0.9
CA B:GLY97 4.2 35.2 1.0
OE1 B:GLU166 4.2 61.4 1.0
N B:ALA96 4.3 31.1 1.0
CA B:ALA96 4.3 31.8 1.0
O B:HOH413 4.3 34.4 1.0
O B:HOH453 4.4 46.5 1.0
OE2 B:GLU112 4.4 38.8 1.0
CD B:GLN82 4.4 36.6 1.0
CG B:GLU116 4.6 36.0 1.0
CD B:GLU166 4.8 61.5 1.0
CB B:ALA96 4.8 31.9 1.0
CZ B:ARG84 4.8 34.9 1.0
NH1 B:ARG84 4.9 35.2 1.0

Magnesium binding site 4 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 4 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
B:Mg304

b:81.4
occ:1.00
 OE2 B:GLU112 2.6 38.8 1.0
OE2 B:GLU115 2.7 41.2 1.0
OE1 B:GLU166 2.9 61.4 1.0
O B:HOH421 2.9 56.8 1.0
O B:HOH433 3.0 60.0 1.0
OE2 B:GLU166 3.3 61.9 1.0
CB B:GLU115 3.4 39.5 1.0
CD B:GLU112 3.5 38.7 1.0
CD B:GLU166 3.5 61.5 1.0
CG B:GLU116 3.5 36.0 1.0
OE2 B:GLU116 3.7 35.4 1.0
CD B:GLU115 3.7 41.0 1.0
OE1 B:GLU112 3.7 40.1 1.0
O B:HOH434 3.8 37.5 1.0
CD B:GLU116 4.0 36.0 1.0
CG B:GLU115 4.2 40.1 1.0
O B:GLU112 4.5 35.9 1.0
CA B:GLU112 4.6 37.4 1.0
N B:GLU116 4.6 37.0 1.0
CA B:GLU115 4.7 38.5 1.0
C B:GLU115 4.7 38.0 1.0
CG B:GLU112 4.7 38.3 1.0
OE1 B:GLU115 4.8 41.9 1.0
CB B:GLU116 4.8 36.1 1.0
CB B:GLU112 4.9 38.0 1.0
CG B:GLU166 5.0 61.1 1.0

Magnesium binding site 5 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 5 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 5 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg302

b:50.2
occ:1.00
 MG C:MG303 2.2 39.0 1.0
OE2 C:GLU116 2.9 35.2 1.0
O C:HOH432 2.9 35.3 1.0
O C:ALA96 3.0 32.9 1.0
OE2 C:GLU166 3.0 57.0 1.0
O C:HOH409 3.1 51.1 1.0
O C:HOH423 3.2 57.6 1.0
OE1 C:GLU166 3.2 56.5 1.0
O C:HOH439 3.2 32.7 1.0
CD C:GLU166 3.4 56.4 1.0
OE2 C:GLU112 3.4 38.9 1.0
O C:HOH421 3.5 51.4 1.0
CA C:GLY97 3.6 35.9 1.0
OE1 C:GLU112 3.8 39.9 1.0
CD C:GLU112 3.9 39.0 1.0
C C:ALA96 4.0 32.8 1.0
CD C:GLU116 4.1 35.2 1.0
N C:GLY97 4.2 34.4 1.0
O C:HOH436 4.2 31.6 1.0
CG C:GLU166 4.7 55.5 1.0
C C:GLY97 4.8 37.5 1.0
OE1 C:GLU116 4.9 34.9 1.0
CG C:GLU116 4.9 35.1 1.0
N C:LEU98 5.0 39.5 1.0

Magnesium binding site 6 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 6 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 6 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
C:Mg303

b:39.0
occ:1.00
 O C:HOH439 1.9 32.7 1.0
O C:HOH432 2.0 35.3 1.0
O C:HOH436 2.1 31.6 1.0
MG C:MG302 2.2 50.2 1.0
OE2 C:GLU116 2.3 35.2 1.0
O C:ALA96 2.3 32.9 1.0
CD C:GLU116 3.4 35.2 1.0
C C:ALA96 3.4 32.8 1.0
OE1 C:GLU116 3.7 34.9 1.0
NH2 C:ARG84 3.9 37.0 1.0
OE1 C:GLU166 4.0 56.5 1.0
CA C:GLY97 4.2 35.9 1.0
N C:GLY97 4.2 34.4 1.0
NE2 C:GLN82 4.3 32.0 1.0
CA C:ALA96 4.4 31.6 1.0
N C:ALA96 4.4 30.4 1.0
CD C:GLU166 4.5 56.4 1.0
OE2 C:GLU112 4.6 38.9 1.0
OE1 C:GLN82 4.6 32.2 1.0
OE2 C:GLU166 4.6 57.0 1.0
CG C:GLU116 4.7 35.1 1.0
CZ C:ARG84 4.7 37.3 1.0
NH1 C:ARG84 4.7 37.4 1.0
O C:HOH423 4.8 57.6 1.0
CB C:ALA96 4.8 31.3 1.0
CD C:GLN82 4.9 32.6 1.0
O C:HOH421 4.9 51.4 1.0

Magnesium binding site 7 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 7 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 7 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg301

b:35.1
occ:1.00
 O D:HOH406 2.2 37.2 1.0
OE2 D:GLU116 2.2 70.2 1.0
MG D:MG302 2.3 52.7 1.0
O D:ALA96 2.9 38.4 1.0
O D:HOH422 3.0 43.0 1.0
CD D:GLU116 3.3 70.5 1.0
OE2 D:GLU166 3.3 82.2 1.0
OE2 D:GLU112 3.7 73.5 1.0
OE1 D:GLU116 3.8 70.6 1.0
CD D:GLU166 3.9 82.3 1.0
C D:ALA96 4.0 40.2 1.0
N D:ALA96 4.4 39.1 1.0
OE1 D:GLU166 4.4 82.7 1.0
OE1 D:GLN82 4.6 43.2 1.0
CG D:GLU116 4.6 70.3 1.0
CG D:GLU166 4.6 81.6 1.0
CD D:GLU112 4.6 74.3 1.0
CG1 D:VAL168 4.8 70.0 1.0
CA D:ALA96 4.8 39.5 1.0
NE2 D:GLN82 4.8 42.8 1.0
N D:GLY97 5.0 41.5 1.0

Magnesium binding site 8 out of 8 in 5qk0

Go back to Magnesium Binding Sites List in 5qk0
Magnesium binding site 8 out of 8 in the Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 8 of Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) -- Crystal Structure of NUDT5 in Complex with Z1270312110 within 5.0Å range:
probe atom residue distance (Å) B Occ
D:Mg302

b:52.7
occ:1.00
 O D:HOH422 2.0 43.0 1.0
OE2 D:GLU112 2.2 73.5 1.0
OE2 D:GLU166 2.3 82.2 1.0
MG D:MG301 2.3 35.1 1.0
O D:ALA96 2.8 38.4 1.0
CD D:GLU112 3.4 74.3 1.0
CD D:GLU166 3.4 82.3 1.0
O D:HOH413 3.5 46.3 1.0
OE2 D:GLU116 3.6 70.2 1.0
CA D:GLY97 3.6 42.8 1.0
C D:ALA96 3.7 40.2 1.0
OE1 D:GLU166 4.1 82.7 1.0
N D:GLY97 4.1 41.5 1.0
O D:HOH406 4.1 37.2 1.0
OE1 D:GLU112 4.2 75.2 1.0
CG D:GLU112 4.3 74.2 1.0
CD D:GLU116 4.5 70.5 1.0
CG D:GLU166 4.5 81.6 1.0
OE1 D:GLU116 4.8 70.6 1.0
O D:HOH410 4.8 68.2 1.0
C D:GLY97 4.9 44.3 1.0

Reference:

Y.Dubianok, P.Collins, T.Krojer, N.Wright, C.Strain-Damerell, N.Burgess-Brown, C.Bountra, C.H.Arrowsmith, A.Edwards, K.Huber, F.Von Delft. Pandda Analysis Group Deposition of Models with Modelled Events (E.G. Bound Ligands) To Be Published.
Page generated: Mon Sep 30 02:26:31 2024

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